The traffic flow control strategy is crucial to properly discharge a queue at a bottleneck. In particular, breakdown prevention is a key objective to maintain high-throughput traffic. Many researchers have studied variable speed limit (VSL) algorithms for their own purposes. However, previous VSL studies have mainly focused on traffic safety aspects, and fluctuation mechanisms depending on VSL algorithms have not been fully investigated. In this study, we designed a VSL algorithm to adjust the density (or occupancy) to the optimal range to increase the throughput of the bottleneck. Demand-capacity analysis and simulation results indicate that flow reduction is achieved through VSL. VSL temporarily mitigates input flows by delaying the downstream arrival time. In addition, the results confirm that VSL can effectively control the traffic density to properly handle the congestion of a given merging bottleneck. According to previous research studies and empirical data analysis, there is a relationship between critical density (occupancy) and breakdown. The VSL algorithm clearly shows that throughput at a merging bottleneck can increase through density control. This mechanism sheds some light on traffic control using VSL, which could be adopted in the foreseeable future.